Structure of PDB 8s9c Chain A

Receptor sequence

>8s9cA (length=1273) Species: 9606 (Homo sapiens)

GPQSFVHFTKQSLALIEQRIAERKSKEPKPSSDLEAGKQLPFIYGDIPPG
MVSEPLEDLDPYYADKKTFIVLNKGKTIFRFNATPALYMLSPFSPLRRIS
IKILVHSLFSMLIMCTILTNCIFMTMNNPPDWTKNVEYTFTGIYTFESLV
KILARGFCVGEFTFLRDPWNWLDFVVIVFAYLTEFVNNVSALRTFRVLRA
LKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLSVFALIGLQLFMGNL
KHKCFRNSLENNETLESIMNTLESEEDFRKYFYYLEGSKDALLCGFSTDS
GQCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQDYWENLYQQTL
RAAGKTYMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQANIEEAKQPYW
IKFKKCIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEEFKNVLAIGN
LVFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTLSLVELFLLSVLR
SFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGM
QLFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIVFRVLCGEWIETMWDC
MEVAGQAMCLIVYMMVMVIGNLVVLNLFLALLLSSFSSDNLTAIEEDPDA
NNLQIAVTRIKKGINYVKQTLREFILKAFGKIWWNIRKTCYKIVEHSWFE
SFIVLMILLSSGALAFEDIYIERKKTIKIILEYADKIFTYIFILEMLLKW
IAYGYKTYFTNAWCWLDFLIVDVSLVTLVANTLGYSDLGPIKSLRTLRAL
RPLRALSRFEGMRVVVNALIGAIPSIMNVLLVCLIFWLIFSIMGVNLFAG
KFYECINTTDGSRFPASQVPNRSECFALMNVSQNVRWKNLKVNFDNVGLG
YLSLLQVATFKGWTIIMYAAVDSVNVDKQPKYEYSLYMYIYFVVFIIFGS
FFTLNLFIGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQK
PIPRPGNKIQGCIFDLVTNQAFDISIMVLICLNMVTMMVEKEGQSQHMTE
VLYWINVVFIILFTGECVLKLISLRHYYFTVGWNIFDFVVVIISIVGMFL
ADLIETYFVSPTLFRVIRLARIGRILRLVKGAKGIRTLLFALMMSLPALF
NIGLLLFLVMFIYAIFGMSNFAYVKKEDGINDMFNFETFGNSMICLFQIT
TSAGWDGLLAPILNSKPPDCDPKKVHPGSSVEGDCGNPSVGIFYFVSYII
ISFLVVVNMYIAVILENFSVATE

3D structure

• PDB: 8s9c Structural mapping of Na v 1.7 antagonists.
• Chain: A
• Resolution: 3.2 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	N6W	A	L967 L968 F971 I1457 L1760	L632 L633 F636 I962 L1265
BS02	P5S	A	W1179 R1182 W1245 I1246 G1249 Y1250	W684 R687 W750 I751 G754 Y755
BS03	Y01	A	K1251 F1254	K756 F759
BS04	Y01	A	V755 T758 L759 S848 W849 I1330	V425 T428 L429 S513 W514 I835
BS05	Y01	A	V833 M1338 Y1429 S1430 Y1432 M1433 I1435	V498 M843 Y934 S935 Y937 M938 I940
BS06	LPE	A	S1734 S1742 I1745	S1239 S1247 I1250
BS07	LPE	A	A1257 W1258	A762 W763
BS08	P5S	A	G1489 G1577 W1578 F1581 R1631 T1632 L1634	G994 G1082 W1083 F1086 R1136 T1137 L1139
BS09	LPE	A	E1477 Q1478 Y1481	E982 Q983 Y986
BS10	LPE	A	Y1481 M1485	Y986 M990
BS11	LPE	A	D320 K376 T377	D299 K355 T356
BS12	LPE	A	A1210 F1211 M1307	A715 F716 M812
BS13	LPE	A	S257 A1627	S236 A1132
BS14	LPE	A	W1178 W1179 Y1250	W683 W684 Y755
BS15	P5S	A	L1566 R1570 H1571	L1071 R1075 H1076
BS16	Y01	A	A762 P767	A432 P437
BS17	LPE	A	I1188 H1191 F1194 F1197	I693 H696 F699 F702

Gene Ontology

Molecular Function

• GO:0005216 monoatomic ion channel activity
• GO:0005248 voltage-gated sodium channel activity
• GO:0005261 monoatomic cation channel activity
• GO:0005272 sodium channel activity
• GO:0005515 protein binding

Biological Process

• GO:0006811 monoatomic ion transport
• GO:0006814 sodium ion transport
• GO:0006954 inflammatory response
• GO:0007623 circadian rhythm
• GO:0009636 response to toxic substance
• GO:0009791 post-embryonic development
• GO:0019228 neuronal action potential
• GO:0019233 sensory perception of pain
• GO:0034220 monoatomic ion transmembrane transport
• GO:0035725 sodium ion transmembrane transport
• GO:0048266 behavioral response to pain
• GO:0050965 detection of temperature stimulus involved in sensory perception of pain
• GO:0050974 detection of mechanical stimulus involved in sensory perception
• GO:0055085 transmembrane transport
• GO:0086002 cardiac muscle cell action potential involved in contraction
• GO:0098870 action potential propagation

Cellular Component

• GO:0001518 voltage-gated sodium channel complex
• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0030424 axon
• GO:0033268 node of Ranvier
• GO:0034702 monoatomic ion channel complex
• GO:0042995 cell projection
• GO:0043005 neuron projection
• GO:0043679 axon terminus

External links

• PDB: RCSB:8s9c, PDBe:8s9c, PDBj:8s9c
• PDBsum: 8s9c
• PubMed: 37270609
• UniProt: Q15858|SCN9A_HUMAN Sodium channel protein type 9 subunit alpha (Gene Name=SCN9A)